Contacts of the helix formed by residues 62 - 77 (chain H) in PDB entry 3CME
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 62 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PRO* 5.3 5.3 - - + +
28H GLY 3.3 15.4 + - - -
29H SER* 3.6 13.9 - - - +
30H LYS* 2.8 56.9 - - + +
31H ILE* 3.8 6.0 - - + +
60H LEU 3.5 2.6 + - - -
61H ARG* 1.3 73.0 - - + +
63H GLY* 1.3 59.2 + - - +
65H LEU* 3.6 14.6 - - - +
66H GLU* 2.8 30.7 + - - +
94H PRO* 4.4 5.8 - - + -
124H VAL 5.4 0.4 - - - -
125H GLY* 4.1 9.4 - - - -
126H THR* 2.9 53.7 + - - +
127H ALA* 4.4 0.4 - - - +
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Residues in contact with GLY 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25180 C 5.4 0.2 + - - -
25190 C 3.6 18.0 - - - +
30H LYS* 4.1 24.5 - - - -
61H ARG* 2.8 6.7 + - - +
62H HIS* 1.3 82.9 + - - +
64H SER* 1.3 57.5 + - - +
66H GLU* 3.6 4.2 - - - +
67H ALA* 3.0 28.1 + - - +
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Residues in contact with SER 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25190 C 3.0 12.4 + - - -
25200 G 2.7 33.3 + - - -
60H LEU* 4.7 9.4 - - - -
61H ARG* 2.4 36.2 + - - +
63H GLY* 1.3 67.7 - - - -
65H LEU* 1.3 64.5 + - - -
66H GLU 3.0 2.0 + - - -
67H ALA* 3.4 1.2 + - - +
68H SER* 3.1 25.8 + - - -
159H LYS 4.0 13.0 - - - +
160H ILE* 4.4 6.9 - - - +
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Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ILE* 3.5 28.3 - - + -
60H LEU* 2.8 66.4 - - + +
61H ARG 3.1 15.8 + - - +
62H HIS* 3.6 6.5 - - + +
64H SER* 1.3 79.4 - - - +
66H GLU* 1.3 58.8 + - - +
68H SER* 3.3 5.2 + - - -
69H ARG* 2.9 29.8 + - - +
90H LEU* 4.1 12.5 - - + +
92H LYS* 5.3 3.8 - - + +
94H PRO* 4.9 2.7 - - + -
128H ALA* 4.1 15.7 - - + +
136H LEU* 4.1 21.1 - - + -
137H PHE* 4.3 0.4 - - - -
160H ILE* 5.5 0.7 - - + -
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Residues in contact with GLU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LYS* 2.6 34.0 - - + +
31H ILE* 2.8 9.5 - - - +
32H ALA* 2.6 25.6 + - - +
62H HIS 2.8 17.9 + - - +
63H GLY* 3.6 7.4 - - - +
64H SER 3.0 0.8 - - - -
65H LEU* 1.3 75.3 - - - +
67H ALA* 1.3 58.9 + - - +
69H ARG* 2.9 31.3 + - - +
70H LEU* 2.7 57.8 + - + +
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Residues in contact with ALA 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25180 C 4.2 11.7 - - - +
25190 C 3.2 40.6 - - - +
63H GLY 3.0 11.6 + - - +
64H SER 3.9 0.7 - - - +
66H GLU* 1.3 80.0 - - - +
68H SER* 1.3 62.5 + - - +
70H LEU* 3.5 8.7 - - - +
71H SER* 3.0 26.0 + - - -
159H LYS* 3.7 13.7 + - + +
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Residues in contact with SER 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H SER 3.1 11.4 + - - -
65H LEU* 3.3 10.9 + - - -
67H ALA* 1.3 75.0 - - - +
69H ARG* 1.3 76.8 + - - +
70H LEU 3.0 0.2 + - - -
71H SER* 2.7 23.1 + - - -
72H ALA* 2.9 12.1 + - - +
136H LEU* 5.0 0.3 - - - +
137H PHE* 3.5 15.1 - - - -
156H ALA* 3.4 34.2 - - - +
159H LYS* 4.0 7.6 - - - +
160H ILE* 3.9 14.2 - - - +
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Residues in contact with ARG 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ILE* 4.2 1.8 - - - -
32H ALA* 3.1 21.6 - - - +
33H GLN* 2.8 67.5 + - - +
36H MET* 3.3 34.6 - - + -
65H LEU 2.9 19.5 - - - +
66H GLU* 2.9 14.2 + - - +
68H SER* 1.3 80.5 + - - +
70H LEU* 1.3 99.6 + - - +
72H ALA* 3.8 2.8 - - - +
73H ASN* 3.1 23.5 + - - +
88H MET* 4.1 0.7 - - - +
90H LEU* 3.9 9.2 - - + -
137H PHE* 3.4 24.0 - - + -
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ALA* 5.8 0.7 - - + -
66H GLU* 2.7 36.6 + - + +
67H ALA* 3.5 8.5 - - - +
68H SER 3.0 0.2 + - - -
69H ARG* 1.3 99.7 - - - +
71H SER* 1.3 52.8 + - - +
72H ALA 2.6 14.6 + - - -
73H ASN* 3.8 0.8 - - - +
74H ARG* 2.7 55.7 + - + +
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25020 C 6.0 0.7 - - - -
67H ALA 3.0 11.6 + - - -
68H SER* 2.7 23.9 + - - -
70H LEU* 1.3 78.0 - - - +
72H ALA* 1.3 61.6 + - - +
74H ARG* 3.8 21.4 - - - +
75H HIS* 3.4 17.0 + - - +
155H ARG* 3.9 33.1 + - - -
159H LYS* 4.0 21.6 - - - +
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Residues in contact with ALA 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H SER 2.9 17.2 + - - +
69H ARG* 3.8 4.3 - - - +
70H LEU 2.6 4.6 + - - -
71H SER* 1.3 70.6 + - - +
73H ASN* 1.3 66.8 + - - +
74H ARG 3.0 0.9 - - - -
75H HIS* 2.8 18.5 + - - +
76H LEU* 3.0 8.9 + - - -
88H MET* 4.2 13.9 - - + -
137H PHE* 5.7 1.6 - - + -
152H ALA* 3.5 39.0 - - + +
153H PHE* 4.7 2.9 - - + +
156H ALA* 4.1 10.8 - - + -
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Residues in contact with ASN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLN* 6.0 1.1 + - - -
36H MET* 2.9 41.7 - - - +
37H GLY 4.3 0.2 - - - +
69H ARG* 3.1 16.9 + - - +
70H LEU* 2.9 4.5 + - - +
72H ALA* 1.3 77.1 - - - +
74H ARG* 1.3 63.7 + - - +
76H LEU* 3.0 8.8 + - - +
77H ILE* 2.8 43.0 + - - +
86H TYR* 3.1 22.5 + - - -
88H MET* 3.6 15.7 - - + +
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Residues in contact with ARG 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25040 A 2.6 68.6 + - - -
25170 A 4.8 8.7 + - - -
70H LEU* 2.7 50.6 + - + +
71H SER* 3.8 24.6 - - - +
73H ASN* 1.3 73.5 + - - +
75H HIS* 1.3 65.6 + - - +
77H ILE* 2.8 25.1 + - - +
78H LYS* 3.5 10.4 + - - +
155H ARG* 6.0 0.4 - - - +
159H LYS* 4.8 9.3 - - - +
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Residues in contact with HIS 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H SER 3.4 10.6 + - - +
72H ALA 2.8 15.3 + - - +
74H ARG* 1.3 75.9 - - - +
76H LEU* 1.3 52.9 + - - +
78H LYS* 3.0 21.9 + - + +
79H GLU* 2.7 64.2 + - + +
148H HIS* 3.8 24.9 + - + -
151H GLU* 3.7 26.8 - - + +
152H ALA* 4.3 8.7 - - + -
155H ARG* 3.9 31.8 + - - +
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ALA 3.0 5.0 + - - +
73H ASN* 3.0 14.2 + - - +
75H HIS* 1.3 76.2 - - - +
77H ILE* 1.3 62.2 + - - +
79H GLU* 4.7 1.1 - - - +
80H LEU* 3.2 51.1 - - + +
81H GLY 3.9 0.2 + - - -
86H TYR* 3.8 39.3 - - + -
88H MET* 4.1 26.5 - - + -
139H ALA* 5.0 2.2 - - + -
145H ASP 5.3 0.2 - - - +
148H HIS* 4.2 6.7 - - + +
149H VAL* 4.0 35.0 - - + +
152H ALA* 4.0 14.6 - - + -
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Residues in contact with ILE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ASN* 2.8 31.3 + - - +
74H ARG* 2.8 20.6 + - - +
76H LEU* 1.3 69.2 - - - +
78H LYS* 2.6 43.9 - - - -
79H GLU 2.8 3.8 + - - -
81H GLY* 2.8 29.5 + - - +
82H GLU* 3.9 33.9 - - + +
86H TYR* 3.7 13.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il